A citation-based method for searching scientific literature

Timothy Gilpatrick, Isac Lee, James E Graham, Etienne Raimondeau, Rebecca Bowen, Andrew Heron, Bradley Downs, Saraswati Sukumar, Fritz J Sedlazeck, Winston Timp. Nat Biotechnol 2020
Times Cited: 71







List of co-cited articles
441 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity



Detecting DNA cytosine methylation using nanopore sequencing.
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp. Nat Methods 2017
305
35

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
657
25

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
25

Accurate detection of complex structural variations using single-molecule sequencing.
Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, Michael C Schatz. Nat Methods 2018
390
21

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nicholas J Loman, Joshua Quick, Jared T Simpson. Nat Methods 2015
535
15

Performance of neural network basecalling tools for Oxford Nanopore sequencing.
Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
214
15

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing.
Pay Giesselmann, Björn Brändl, Etienne Raimondeau, Rebecca Bowen, Christian Rohrandt, Rashmi Tandon, Helene Kretzmer, Günter Assum, Christina Galonska, Reiner Siebert,[...]. Nat Biotechnol 2019
37
29

Mapping DNA methylation with high-throughput nanopore sequencing.
Arthur C Rand, Miten Jain, Jordan M Eizenga, Audrey Musselman-Brown, Hugh E Olsen, Mark Akeson, Benedict Paten. Nat Methods 2017
179
14


Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins,[...]. Nat Commun 2019
247
14

Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
166
14

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
426
12

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
12

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder. Genome Biol 2018
183
12

Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications.
Christopher M Watson, Laura A Crinnion, Sarah Hewitt, Jennifer Bates, Rachel Robinson, Ian M Carr, Eamonn Sheridan, Julian Adlard, David T Bonthron. Lab Invest 2020
11
81

Using long-read sequencing to detect imprinted DNA methylation.
Scott Gigante, Quentin Gouil, Alexis Lucattini, Andrew Keniry, Tamara Beck, Matthew Tinning, Lavinia Gordon, Chris Woodruff, Terence P Speed, Marnie E Blewitt,[...]. Nucleic Acids Res 2019
39
23

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
12

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren,[...]. Nat Biotechnol 2020
79
12

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson,[...]. Nat Biotechnol 2019
269
12

Real-time, portable genome sequencing for Ebola surveillance.
Joshua Quick, Nicholas J Loman, Sophie Duraffour, Jared T Simpson, Ettore Severi, Lauren Cowley, Joseph Akoi Bore, Raymond Koundouno, Gytis Dudas, Amy Mikhail,[...]. Nature 2016
606
11

Real-time selective sequencing using nanopore technology.
Matthew Loose, Sunir Malla, Michael Stout. Nat Methods 2016
91
11

Highly parallel direct RNA sequencing on an array of nanopores.
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland,[...]. Nat Methods 2018
343
11

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan,[...]. Nat Commun 2017
140
11

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
11


Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH).
Tslil Gabrieli, Hila Sharim, Dena Fridman, Nissim Arbib, Yael Michaeli, Yuval Ebenstein. Nucleic Acids Res 2018
41
19

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, Michael C Schatz. Nat Biotechnol 2021
30
26

Long-read human genome sequencing and its applications.
Glennis A Logsdon, Mitchell R Vollger, Evan E Eichler. Nat Rev Genet 2020
93
11

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Qian Liu, Li Fang, Guoliang Yu, Depeng Wang, Chuan-Le Xiao, Kai Wang. Nat Commun 2019
89
11

Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
614
9

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing.
Kornel Labun, Tessa G Montague, Maximilian Krause, Yamila N Torres Cleuren, Håkon Tjeldnes, Eivind Valen. Nucleic Acids Res 2019
251
9

NanoPack: visualizing and processing long-read sequencing data.
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. Bioinformatics 2018
435
9

Nucleic acid detection with CRISPR-Cas13a/C2c2.
Jonathan S Gootenberg, Omar O Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M Daringer, Catherine A Freije,[...]. Science 2017
840
9

Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
564
9

CRISPR/Cas9-targeted enrichment and long-read sequencing of the Fuchs endothelial corneal dystrophy-associated TCF4 triplet repeat.
Nathaniel J Hafford-Tear, Yu-Chih Tsai, Amanda N Sadan, Beatriz Sanchez-Pintado, Christina Zarouchlioti, Geoffrey J Maher, Petra Liskova, Stephen J Tuft, Alison J Hardcastle, Tyson A Clark,[...]. Genet Med 2019
23
30

Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing.
Christina Stangl, Sam de Blank, Ivo Renkens, Liset Westera, Tamara Verbeek, Jose Espejo Valle-Inclan, Rocio Chamorro González, Anton G Henssen, Markus J van Roosmalen, Ronald W Stam,[...]. Nat Commun 2020
9
77

Multiplex genome engineering using CRISPR/Cas systems.
Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu, Wenyan Jiang, Luciano A Marraffini,[...]. Science 2013
9

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning.
Peng Ni, Neng Huang, Zhi Zhang, De-Peng Wang, Fan Liang, Yu Miao, Chuan-Le Xiao, Feng Luo, Jianxin Wang. Bioinformatics 2019
57
12

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Norah Sadowski, Fritz J Sedlazeck, Kasper D Hansen, Jared T Simpson, Winston Timp. Nat Methods 2020
25
28

Three decades of nanopore sequencing.
David Deamer, Mark Akeson, Daniel Branton. Nat Biotechnol 2016
311
8

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.
Adrian Viehweger, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth Madhugiri, John Ziebuhr, Martin Hölzer, Manja Marz. Genome Res 2019
75
8

NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.
Arne De Roeck, Wouter De Coster, Liene Bossaerts, Rita Cacace, Tim De Pooter, Jasper Van Dongen, Svenn D'Hert, Peter De Rijk, Mojca Strazisar, Christine Van Broeckhoven,[...]. Genome Biol 2019
23
26

SVIM: structural variant identification using mapped long reads.
David Heller, Martin Vingron. Bioinformatics 2019
47
12

Characterizing the Major Structural Variant Alleles of the Human Genome.
Peter A Audano, Arvis Sulovari, Tina A Graves-Lindsay, Stuart Cantsilieris, Melanie Sorensen, AnneMarie E Welch, Max L Dougherty, Bradley J Nelson, Ankeeta Shah, Susan K Dutcher,[...]. Cell 2019
153
8



Readfish enables targeted nanopore sequencing of gigabase-sized genomes.
Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat J Debebe, Matthew Loose. Nat Biotechnol 2021
23
26

Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E Workman, Alison D Tang, Paul S Tang, Miten Jain, John R Tyson, Roham Razaghi, Philip C Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick,[...]. Nat Methods 2019
126
7

Accurate detection of m6A RNA modifications in native RNA sequences.
Huanle Liu, Oguzhan Begik, Morghan C Lucas, Jose Miguel Ramirez, Christopher E Mason, David Wiener, Schraga Schwartz, John S Mattick, Martin A Smith, Eva Maria Novoa. Nat Commun 2019
120
7


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.